Merge branch 'edge' into abr-plate-reader-tart

Makefile

@@ -152,6 +152,10 @@ push:
 	sleep 1
 	$(MAKE) -C $(UPDATE_SERVER_DIR) push
 
+.PHONY: push-folder
+PUSH_HELPER := abr-testing/abr_testing/tools/make_push.py
+push-folder:
+	$(OT_PYTHON) $(PUSH_HELPER)
 
 .PHONY: push-ot3
 push-ot3:

abr-testing/abr_testing/data_collection/abr_calibration_logs.py

@@ -286,6 +286,7 @@ def run(
     ip_json_file = os.path.join(storage_directory, "IPs.json")
     try:
         ip_file = json.load(open(ip_json_file))
+        robot_dict = ip_file.get("ip_address_list")
     except FileNotFoundError:
         print(f"Add .json file with robot IPs to: {storage_directory}.")
         sys.exit()
@@ -294,7 +295,7 @@ def run(
         ip_or_all = input("IP Address or ALL: ")
         calibration_data = []
         if ip_or_all.upper() == "ALL":
-            ip_address_list = ip_file["ip_address_list"]
+            ip_address_list = list(robot_dict.keys())
             for ip in ip_address_list:
                 saved_file_path, calibration = read_robot_logs.get_calibration_offsets(
                     ip, storage_directory

abr-testing/abr_testing/data_collection/get_run_logs.py

@@ -104,10 +104,11 @@ def get_all_run_logs(
     ip_json_file = os.path.join(storage_directory, "IPs.json")
     try:
         ip_file = json.load(open(ip_json_file))
+        robot_dict = ip_file.get("ip_address_list")
     except FileNotFoundError:
         print(f"Add .json file with robot IPs to: {storage_directory}.")
         sys.exit()
-    ip_address_list = ip_file["ip_address_list"]
+    ip_address_list = list(robot_dict.keys())
     runs_from_storage = read_robot_logs.get_run_ids_from_google_drive(google_drive)
     for ip in ip_address_list:
         runs = get_run_ids_from_robot(ip)

abr-testing/abr_testing/protocol_simulation/abr_sim_check.py

@@ -46,7 +46,7 @@ def get_files() -> Tuple[Dict[str, Dict[str, Union[str, Path]]], List[Path]]:
     labware_defs = []
     for root, directories, _ in os.walk(root_dir):
         for directory in directories:
-            if directory == "active_protocols":
+            if directory not in exclude:
                 active_dir = os.path.join(root, directory)
                 for file in os.listdir(
                     active_dir
@@ -100,7 +100,6 @@ def get_files() -> Tuple[Dict[str, Dict[str, Union[str, Path]]], List[Path]]:
     exclude = [
         "__init__.py",
         "helpers.py",
-        "shared_vars_and_funcs.py",
     ]
     print("Simulating Protocols")
     file_dict, labware_defs = get_files()

abr-testing/abr_testing/tools/make_push.py

@@ -0,0 +1,95 @@
+"""Push one or more folders to one or more robots."""
+import subprocess
+import multiprocessing
+import json
+
+global folders
+# Opentrons folders that can be pushed to robot
+folders = [
+    "abr-testing",
+    "hardware-testing",
+    "abr-testing + hardware-testing",
+    "other",
+]
+
+
+def push_subroutine(cmd: str) -> None:
+    """Pushes specified folder to specified robot."""
+    try:
+        subprocess.run(cmd)
+    except Exception:
+        print("failed to push folder")
+        raise
+
+
+def main(folder_to_push: str, robot_to_push: str) -> int:
+    """Main process!"""
+    cmd = "make -C {folder} push-ot3 host={ip}"
+    robot_ip_path = ""
+    push_cmd = ""
+    folder_int = int(folder_to_push)
+    if folders[folder_int].lower() == "abr-testing + hardware-testing":
+        if robot_to_push.lower() == "all":
+            robot_ip_path = input("Path to robot ips: ")
+            with open(robot_ip_path, "r") as ip_file:
+                robot_json = json.load(ip_file)
+                robot_ips_dict = robot_json.get("ip_address_list")
+                robot_ips = list(robot_ips_dict.keys())
+                ip_file.close()
+        else:
+            robot_ips = [robot_to_push]
+        for folder_name in folders[:-2]:
+            # Push abr-testing and hardware-testing folders to all robots
+            for robot in robot_ips:
+                print_proc = multiprocessing.Process(
+                    target=print, args=(f"Pushing {folder_name} to {robot}!\n\n",)
+                )
+                print_proc.start()
+                print_proc.join()
+                push_cmd = cmd.format(folder=folder_name, ip=robot)
+                process = multiprocessing.Process(
+                    target=push_subroutine, args=(push_cmd,)
+                )
+                process.start()
+                process.join()
+                print_proc = multiprocessing.Process(target=print, args=("Done!\n\n",))
+                print_proc.start()
+                print_proc.join()
+    else:
+
+        if folder_int == (len(folders) - 1):
+            folder_name = input("Which folder? ")
+        else:
+            folder_name = folders[folder_int]
+        if robot_to_push.lower() == "all":
+            robot_ip_path = input("Path to robot ips: ")
+            with open(robot_ip_path, "r") as ip_file:
+                robot_json = json.load(ip_file)
+                robot_ips = robot_json.get("ip_address_list")
+            ip_file.close()
+        else:
+            robot_ips = [robot_to_push]
+
+        # Push folder to robots
+        for robot in robot_ips:
+            print_proc = multiprocessing.Process(
+                target=print, args=(f"Pushing {folder_name} to {robot}!\n\n",)
+            )
+            print_proc.start()
+            print_proc.join()
+            push_cmd = cmd.format(folder=folder_name, ip=robot)
+            process = multiprocessing.Process(target=push_subroutine, args=(push_cmd,))
+            process.start()
+            process.join()
+            print_proc = multiprocessing.Process(target=print, args=("Done!\n\n",))
+            print_proc.start()
+            print_proc.join()
+    return 0
+
+
+if __name__ == "__main__":
+    for i, folder in enumerate(folders):
+        print(f"{i}) {folder}")
+    folder_to_push = input("Please Select a Folder to Push: ")
+    robot_to_push = input("Type in robots ip (type all for all): ")
+    print(main(folder_to_push, robot_to_push))

analyses-snapshot-testing/Makefile

@@ -3,12 +3,12 @@ CACHEBUST ?= $(shell date +%s)
 ANALYSIS_REF ?= edge
 PROTOCOL_NAMES ?= all
 OVERRIDE_PROTOCOL_NAMES ?= all
-OPENTRONS_VERSION ?= edge
+LOCAL_IMAGE_TAG ?= local
+ANALYZER_IMAGE_NAME ?= opentrons-analysis
 
-export OPENTRONS_VERSION # used for server
-export ANALYSIS_REF # used for analysis and snapshot test
-export PROTOCOL_NAMES # used for the snapshot test
-export OVERRIDE_PROTOCOL_NAMES # used for the snapshot test
+export ANALYSIS_REF # tag, branch or commit for the opentrons repository. Used as the image tag for the analyzer image
+export PROTOCOL_NAMES # tell the test which protocols to run
+export OVERRIDE_PROTOCOL_NAMES # tell the test which override protocols to run
 
 ifeq ($(CI), true)
 	PYTHON=python
@@ -93,23 +93,47 @@ build-base-image:
 
 .PHONY: build-opentrons-analysis
 build-opentrons-analysis:
-	@echo "Building docker image for $(ANALYSIS_REF)"
-	@echo "The image will be named opentrons-analysis:$(ANALYSIS_REF)"
-	@echo "If you want to build a different version, run 'make build-opentrons-analysis ANALYSIS_REF=<version>'"
-	docker build --build-arg BASE_IMAGE_NAME=$(BASE_IMAGE_NAME) --build-arg ANALYSIS_REF=$(ANALYSIS_REF) --build-arg CACHEBUST=$(CACHEBUST) -t opentrons-analysis:$(ANALYSIS_REF) -f citools/Dockerfile.analyze citools/.
+	@echo "Building docker image for opentrons repository reference$(ANALYSIS_REF)"
+	@echo "The image will be named $(ANALYZER_IMAGE_NAME):$(ANALYSIS_REF)"
+	@echo "If you want to build a different version, run 'make build-opentrons-analysis ANALYSIS_REF=<tag, branch, or commit>'"
+	docker build --build-arg BASE_IMAGE_NAME=$(BASE_IMAGE_NAME) --build-arg ANALYSIS_REF=$(ANALYSIS_REF) --build-arg CACHEBUST=$(CACHEBUST) -t $(ANALYZER_IMAGE_NAME):$(ANALYSIS_REF) -f citools/Dockerfile.analyze citools/.
 
-.PHONY: local-build
-local-build:
+.PHONY: build-local
+build-local:
 	@echo "Building docker image for your local opentrons code"
-	@echo "The image will be named opentrons-analysis:local"
-	@echo "For a fresh build, run 'make local-build NO_CACHE=1'"
-	docker build --build-arg BASE_IMAGE_NAME=$(BASE_IMAGE_NAME) $(BUILD_FLAGS) -t opentrons-analysis:local -f citools/Dockerfile.local .. || true
+	@echo "This image will be named $(ANALYZER_IMAGE_NAME):$(LOCAL_IMAGE_TAG)"
+	docker build --build-arg BASE_IMAGE_NAME=$(BASE_IMAGE_NAME) -t $(ANALYZER_IMAGE_NAME):$(LOCAL_IMAGE_TAG) -f citools/Dockerfile.local ..
 	@echo "Build complete"
 
+.PHONY: snapshot-test-local
+snapshot-test-local: ANALYSIS_REF=$(LOCAL_IMAGE_TAG)
+snapshot-test-local: build-base-image build-local
+	@echo "This target is overriding the ANALYSIS_REF to the LOCAL_IMAGE_TAG: $(LOCAL_IMAGE_TAG)"
+	@echo "ANALYSIS_REF is $(ANALYSIS_REF). The the test maps this env variable to the image tag."
+	@echo "The image the test will use is $(ANALYZER_IMAGE_NAME):$(LOCAL_IMAGE_TAG)"
+	@echo "PROTOCOL_NAMES is $(PROTOCOL_NAMES)"
+	@echo "OVERRIDE_PROTOCOL_NAMES is $(OVERRIDE_PROTOCOL_NAMES)"
+	$(PYTHON) -m pipenv run pytest -k analyses_snapshot_test -vv
+
+.PHONY: snapshot-test-update-local
+snapshot-test-update-local: ANALYSIS_REF=$(LOCAL_IMAGE_TAG)
+snapshot-test-update-local: build-base-image build-local
+	@echo "This target is overriding the ANALYSIS_REF to the LOCAL_IMAGE_TAG: $(LOCAL_IMAGE_TAG)"
+	@echo "ANALYSIS_REF is $(ANALYSIS_REF). The the test maps this env variable to the image tag."
+	@echo "The image the test will use is $(ANALYZER_IMAGE_NAME):$(LOCAL_IMAGE_TAG)"
+	@echo "PROTOCOL_NAMES is $(PROTOCOL_NAMES)"
+	@echo "OVERRIDE_PROTOCOL_NAMES is $(OVERRIDE_PROTOCOL_NAMES)"
+	$(PYTHON) -m pipenv run pytest -k analyses_snapshot_test --snapshot-update
+
 .PHONY: generate-protocols
 generate-protocols:
 	$(PYTHON) -m pipenv run python -m automation.data.protocol_registry
 
+# Tools for running the robot server in a container
+
+OPENTRONS_VERSION ?= edge
+export OPENTRONS_VERSION # used for the robot server image as the tag, branch or commit for the opentrons repository
+
 .PHONY: build-rs
 build-rs:
 	@echo "Building docker image for opentrons-robot-server:$(OPENTRONS_VERSION)"

analyses-snapshot-testing/README.md

@@ -4,7 +4,7 @@
 
 1. Follow the instructions in [DEV_SETUP.md](../DEV_SETUP.md)
 1. `cd analyses-snapshot-testing`
-1. use pyenv to install python 3.12 and set it as the local python version for this directory
+1. use pyenv to install python 3.13 and set it as the local python version for this directory
 1. `make setup`
 1. Have docker installed and ready
 
@@ -72,10 +72,17 @@ cd analyses-snapshot-testing \
 
 > This copies in your local code to the container and runs the analyses battery against it.
 
-1. `make build-base-image`
-1. `make build-local`
-1. `make local-snapshot-test`
+`cd PYENV_ROOT && git pull` - make sure pyenv is up to date so you may install python 3.13.0
+`pyenv install 3.13.0` - install python 3.13.0
+`cd <OPENTRONS_REPO_ROOT>/analyses-snapshot-testing` - navigate to the analyses-snapshot-testing directory
+`pyenv local 3.13.0` - set the local python version to 3.13.0
+`make setup` - install the requirements
+`make snapshot-test-local` - this target builds the base image, builds the local code into the base image, then runs the analyses battery against the image you just created
 
 You have the option to specify one or many protocols to run the analyses on. This is also described above [Running the tests against specific protocols](#running-the-tests-against-specific-protocols)
 
-- `make local-snapshot-test PROTOCOL_NAMES=Flex_S_v2_19_Illumina_DNA_PCR_Free OVERRIDE_PROTOCOL_NAMES=none`
+- `make snapshot-test-local PROTOCOL_NAMES=Flex_S_v2_19_Illumina_DNA_PCR_Free OVERRIDE_PROTOCOL_NAMES=none`
+
+### Updating the snapshots locally
+
+- `make snapshot-test-update-local` - this target builds the base image, builds the local code into the base image, then runs the analyses battery against the image you just created, updating the snapshots by passing the `--update-snapshots` flag to the test

analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[004ebb2b82][OT2_S_v2_11_P10S_P300M_MM_TC1_TM_Swift].json

@@ -16668,6 +16668,7 @@
       }
     }
   ],
+  "liquidClasses": [],
   "liquids": [],
   "metadata": {
     "apiLevel": "2.11"

analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[00574c503f][pl_BacteriaInoculation_Flex_6plates].json

@@ -41584,6 +41584,7 @@
       "location": "offDeck"
     }
   ],
+  "liquidClasses": [],
   "liquids": [
     {
       "description": "Bacterial culture medium (e.g., LB broth)",

analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[011481812b][OT2_S_v2_7_P20S_None_Walkthrough].json

@@ -4919,6 +4919,7 @@
       }
     }
   ],
+  "liquidClasses": [],
   "liquids": [],
   "metadata": {
     "apiLevel": "2.7",

analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[01255c3f3b][pl_Flex_Protein_Digestion_Protocol].json

@@ -11824,6 +11824,7 @@
       }
     }
   ],
+  "liquidClasses": [],
   "liquids": [],
   "metadata": {
     "author": "<[email protected]>",

analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[0190369ce5][Flex_S_v2_16_P1000_96_GRIP_HS_MB_TC_TM_DeckConfiguration1NoFixtures].json

@@ -11452,6 +11452,7 @@
       }
     }
   ],
+  "liquidClasses": [],
   "liquids": [
     {
       "description": "High Quality H₂O",

analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[0256665840][OT2_S_v2_16_P300M_P20S_aspirateDispenseMix0Volume].json

@@ -2917,6 +2917,7 @@
       }
     }
   ],
+  "liquidClasses": [],
   "liquids": [
     {
       "description": "H₂O",

analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[041ad55e7b][OT2_S_v2_15_P300M_P20S_HS_TC_TM_dispense_changes].json

@@ -3113,6 +3113,7 @@
       }
     }
   ],
+  "liquidClasses": [],
   "liquids": [],
   "metadata": {
     "author": "Opentrons Engineering <[email protected]>",

analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[057de2035d][OT2_S_v2_19_P300M_P20S_HS_TC_TM_SmokeTestV3].json

@@ -9569,6 +9569,7 @@
       }
     }
   ],
+  "liquidClasses": [],
   "liquids": [],
   "metadata": {
     "author": "Opentrons Engineering <[email protected]>",

analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[0903a95825][Flex_S_v2_19_QIASeq_FX_48x].json

@@ -66156,6 +66156,7 @@
       }
     }
   ],
+  "liquidClasses": [],
   "liquids": [],
   "metadata": {
     "author": "Opentrons <[email protected]>",

analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[09676b9f7e][Flex_X_v2_20_96_None_Overrides_TooTallLabware_Override_south_west].json

@@ -1481,6 +1481,7 @@
       }
     }
   ],
+  "liquidClasses": [],
   "liquids": [],
   "metadata": {
     "description": "oooo",

analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[09ba51132a][OT2_S_v2_14_NO_PIPETTES_TC_VerifyThermocyclerLoadedSlots].json

@@ -154,6 +154,7 @@
       }
     }
   ],
+  "liquidClasses": [],
   "liquids": [],
   "metadata": {},
   "modules": [

analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[0a9ef592c8][Flex_S_v2_18_Illumina_DNA_Prep_48x].json

@@ -49707,6 +49707,7 @@
       }
     }
   ],
+  "liquidClasses": [],
   "liquids": [
     {
       "description": "CleanupBead Beads",

analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[0affe60373][Flex_X_v2_18_NO_PIPETTES_Overrides_BadTypesInRTP_Override_wrong_type_in_maximum].json

@@ -42,6 +42,7 @@
     }
   ],
   "labware": [],
+  "liquidClasses": [],
   "liquids": [],
   "metadata": {
     "protocolName": "Description Too Long 2.18"

analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[0b42cfc151][Flex_X_v2_20_96_None_Overrides_TooTallLabware_Override_north_row].json

@@ -1481,6 +1481,7 @@
       }
     }
   ],
+  "liquidClasses": [],
   "liquids": [],
   "metadata": {
     "description": "oooo",

analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[0c4ae179bb][OT2_S_v2_15_P300M_P20S_HS_TC_TM_SmokeTestV3].json

@@ -17072,6 +17072,7 @@
       }
     }
   ],
+  "liquidClasses": [],
   "liquids": [
     {
       "description": "H₂O",

analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[0cbde10c37][OT2_S_v2_18_P300M_P20S_HS_TC_TM_SmokeTestV3].json

@@ -9569,6 +9569,7 @@
       }
     }
   ],
+  "liquidClasses": [],
   "liquids": [],
   "metadata": {
     "author": "Opentrons Engineering <[email protected]>",

analyses-snapshot-testing/tests/__snapshots__/analyses_snapshot_test/test_analysis_snapshot[0dd21c0ee5][pl_EM_seq_48Samples_AllSteps_Edits_150].json

@@ -49392,6 +49392,7 @@
       }
     }
   ],
+  "liquidClasses": [],
   "liquids": [
     {
       "description": "Beads",